Package evaluation to test BiochemicalAlgorithms on Julia 1.14.0-DEV.36 (e2f3178d9b*) started at 2025-11-07T00:12:10.223 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.66s ################################################################################ # Installation # Installing BiochemicalAlgorithms... Resolving package versions... Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed ChunkCodecLibZstd ─────────── v1.0.0 Installed Libuuid_jll ───────────────── v2.41.2+0 Installed Calculus ──────────────────── v0.5.2 Installed InlineStrings ─────────────── v1.4.5 Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed Extents ───────────────────── v0.1.6 Installed OrderedCollections ────────── v1.8.1 Installed PreallocationTools ────────── v0.4.34 Installed RDKitMinimalLib ───────────── v1.2.0 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed Fontconfig_jll ────────────── v2.17.1+0 Installed SentinelArrays ────────────── v1.4.8 Installed NaNMath ───────────────────── v1.1.3 Installed RDKit_jll ─────────────────── v2022.9.5+0 Installed FileIO ────────────────────── v1.17.1 Installed UnitfulAtomic ─────────────── v1.0.0 Installed ScopedValues ──────────────── v1.5.0 Installed Tables ────────────────────── v1.12.1 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed EnumX ─────────────────────── v1.0.5 Installed libinchi_jll ──────────────── v1.6.0+0 Installed Graphics ──────────────────── v1.1.3 Installed PhysicalConstants ─────────── v0.2.4 Installed Jieko ─────────────────────── v0.2.1 Installed InverseFunctions ──────────── v0.1.17 Installed LZO_jll ───────────────────── v2.10.3+0 Installed Reexport ──────────────────── v1.2.2 Installed Mendeleev ─────────────────── v1.0.2 Installed Missings ──────────────────── v1.2.0 Installed TableTraits ───────────────── v1.0.1 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed LaTeXStrings ──────────────── v1.4.0 Installed Preferences ───────────────── v1.5.0 Installed Crayons ───────────────────── v4.1.1 Installed boost_jll ─────────────────── v1.76.0+1 Installed SortingAlgorithms ─────────── v1.2.2 Installed UnPack ────────────────────── v1.0.2 Installed ADTypes ───────────────────── v1.18.0 Installed Inflate ───────────────────── v0.1.5 Installed Format ────────────────────── v1.3.7 Installed RecursiveArrayTools ───────── v3.39.0 Installed DataStructures ────────────── v0.19.3 Installed MacroTools ────────────────── v0.5.16 Installed AbstractTrees ─────────────── v0.4.5 Installed FillArrays ────────────────── v1.15.0 Installed Quaternions ───────────────── v0.7.6 Installed MakieCore ─────────────────── v0.9.5 Installed DelimitedFiles ────────────── v1.9.1 Installed SparseMatrixColorings ─────── v0.4.23 Installed ArnoldiMethod ─────────────── v0.4.0 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed CodecZlib ─────────────────── v0.7.8 Installed ExprTools ─────────────────── v0.1.10 Installed ConsoleProgressMonitor ────── v0.1.2 Installed ArrayInterface ────────────── v7.22.0 Installed Observables ───────────────── v0.5.5 Installed DataValueInterfaces ───────── v1.0.0 Installed Libffi_jll ────────────────── v3.4.7+0 Installed LoggingExtras ─────────────── v1.2.0 Installed Cairo ─────────────────────── v1.1.1 Installed RealDot ───────────────────── v0.1.0 Installed Pixman_jll ────────────────── v0.44.2+0 Installed GPUArraysCore ─────────────── v0.2.0 Installed Expat_jll ─────────────────── v2.7.3+0 Installed libpng_jll ────────────────── v1.6.50+0 Installed SimpleTraits ──────────────── v0.9.5 Installed TerminalLoggers ───────────── v0.1.7 Installed coordgenlibs_jll ──────────── v3.0.2+0 Installed SparseConnectivityTracer ──── v1.1.2 Installed Roots ─────────────────────── v2.2.10 Installed LeftChildRightSiblingTrees ── v0.2.1 Installed MetaGraphs ────────────────── v0.8.1 Installed Setfield ──────────────────── v1.1.2 Installed OptimizationBase ──────────── v2.14.0 Installed PooledArrays ──────────────── v1.4.3 Installed L_BFGS_B_jll ──────────────── v3.0.1+0 Installed PDMats ────────────────────── v0.11.36 Installed Moshi ─────────────────────── v0.3.7 Installed WorkerUtilities ───────────── v1.6.1 Installed TableOperations ───────────── v1.2.0 Installed LBFGSB ────────────────────── v0.4.1 Installed DocStringExtensions ───────── v0.9.5 Installed CompositionsBase ──────────── v0.1.2 Installed CommonSolve ───────────────── v0.2.4 Installed DifferentiationInterface ──── v0.7.10 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed FunctionWrappersWrappers ──── v0.1.3 Installed HashArrayMappedTries ──────── v0.2.0 Installed BiochemicalAlgorithms ─────── v0.5.5 Installed RecipesBase ───────────────── v1.3.4 Installed DataAPI ───────────────────── v1.16.0 Installed InvertedIndices ───────────── v1.3.1 Installed SciMLOperators ────────────── v1.10.0 Installed SciMLStructures ───────────── v1.7.0 Installed Colors ────────────────────── v0.13.1 Installed StaticArraysCore ──────────── v1.4.4 Installed ColorTypes ────────────────── v0.12.1 Installed StringManipulation ────────── v0.4.1 Installed StaticArrays ──────────────── v1.9.15 Installed SciMLPublic ───────────────── v1.0.0 Installed Requires ──────────────────── v1.3.1 Installed MolecularGraph ────────────── v0.19.1 Installed Glib_jll ──────────────────── v2.86.0+0 Installed FunctionWrappers ──────────── v1.1.3 Installed Parsers ───────────────────── v2.8.3 Installed FastClosures ──────────────── v0.3.2 Installed AutoHashEquals ────────────── v2.2.0 Installed JSON ──────────────────────── v0.21.4 Installed SciMLBase ─────────────────── v2.124.0 Installed PrettyTables ──────────────── v2.4.0 Installed BioGenerics ───────────────── v0.1.5 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed WeakRefStrings ────────────── v1.4.2 Installed TestItems ─────────────────── v1.0.0 Installed JLLWrappers ───────────────── v1.7.1 Installed Unitful ───────────────────── v1.25.1 Installed DataFrames ────────────────── v1.8.1 Installed ChunkCodecCore ────────────── v1.0.0 Installed Pango_jll ─────────────────── v1.56.4+0 Installed StructTypes ───────────────── v1.11.0 Installed GeometryBasics ────────────── v0.5.10 Installed IterTools ─────────────────── v1.10.0 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed CSV ───────────────────────── v0.10.15 Installed Accessors ─────────────────── v0.1.42 Installed Measurements ──────────────── v2.14.1 Installed FilePathsBase ─────────────── v0.9.24 Installed JLD2 ──────────────────────── v0.6.2 Installed Graphs ────────────────────── v1.13.1 Installed Adapt ─────────────────────── v4.4.0 Installed BioStructures ─────────────── v4.7.0 Installed RuntimeGeneratedFunctions ─── v0.5.16 Installed Libmount_jll ──────────────── v2.41.2+0 Installed ConstructionBase ──────────── v1.6.0 Installed ChunkSplitters ────────────── v3.1.2 Installed Compat ────────────────────── v4.18.1 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed SymbolicIndexingInterface ─── v0.3.44 Installed TranscodingStreams ────────── v0.11.3 Installed ProgressLogging ───────────── v0.1.5 Installed EarCut_jll ────────────────── v2.2.4+0 Installed CellListMap ───────────────── v0.9.14 Installed StringEncodings ───────────── v0.3.7 Installed Statistics ────────────────── v1.11.1 Installed ProgressMeter ─────────────── v1.11.0 Installed ExproniconLite ────────────── v0.10.14 Installed BioSymbols ────────────────── v5.2.0 Installed PrecompileTools ───────────── v1.3.3 Installed Optimization ──────────────── v4.8.0 Installed ChunkCodecLibZlib ─────────── v1.0.0 Installed YAML ──────────────────────── v0.4.15 Installed Parameters ────────────────── v0.12.3 Installed GettextRuntime_jll ────────── v0.22.4+0 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed JSON3 ─────────────────────── v1.14.3 Installed SciMLLogging ──────────────── v1.4.0 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installed IntervalSets ──────────────── v0.7.11 Installed FixedPointNumbers ─────────── v0.8.5 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed Rotations ─────────────────── v1.7.1 Installing 32 artifacts Installed artifact L_BFGS_B 45.2 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact FreeType2 1.5 MiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact GettextRuntime 543.0 KiB Installed artifact LZO 208.9 KiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact Pango 1.1 MiB Installed artifact coordgenlibs 303.6 KiB Installed artifact Cairo 2.2 MiB Installed artifact libpng 328.4 KiB Installed artifact libinchi 933.4 KiB Installed artifact Graphite2 120.2 KiB Installed artifact Libiconv 1.9 MiB Installed artifact EarCut 80.5 KiB Installed artifact Expat 283.3 KiB Installed artifact Fontconfig 984.8 KiB Installed artifact FriBidi 78.9 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact Bzip2 503.5 KiB Installed artifact Libffi 44.2 KiB Installed artifact Libmount 6.5 MiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Libuuid 3.7 MiB Installed artifact Pixman 372.2 KiB Installed artifact Glib 7.7 MiB Installed artifact boost 22.1 MiB Installed artifact RDKit 56.2 MiB Updating `~/.julia/environments/v1.14/Project.toml` [9d651bdf] + BiochemicalAlgorithms v0.5.5 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] + ADTypes v1.18.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.4.0 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.22.0 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.7.0 [3c28c6f8] + BioSymbols v5.2.0 [9d651bdf] + BiochemicalAlgorithms v0.5.5 [336ed68f] + CSV v0.10.15 [159f3aea] + Cairo v1.1.1 [49dc2e85] + Calculus v0.5.2 [69e1c6dd] + CellListMap v0.9.14 [0b6fb165] + ChunkCodecCore v1.0.0 [4c0bbee4] + ChunkCodecLibZlib v1.0.0 [55437552] + ChunkCodecLibZstd v1.0.0 [ae650224] + ChunkSplitters v3.1.2 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [5ae59095] + 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[076d061b] + HashArrayMappedTries v0.2.0 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.5 [8197267c] + IntervalSets v0.7.11 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [033835bb] + JLD2 v0.6.2 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.3 [ae98c720] + Jieko v0.2.1 [5be7bae1] + LBFGSB v0.4.1 [b964fa9f] + LaTeXStrings v1.4.0 [1d6d02ad] + LeftChildRightSiblingTrees v0.2.1 [e6f89c97] + LoggingExtras v1.2.0 [1914dd2f] + MacroTools v0.5.16 ⌅ [20f20a25] + MakieCore v0.9.5 [eff96d63] + Measurements v2.14.1 [c116f080] + Mendeleev v1.0.2 [626554b9] + MetaGraphs v0.8.1 [e1d29d7a] + Missings v1.2.0 ⌅ [6c89ec66] + MolecularGraph v0.19.1 [2e0e35c7] + Moshi v0.3.7 [77ba4419] + NaNMath v1.1.3 [510215fc] + Observables v0.5.5 ⌅ [7f7a1694] + Optimization v4.8.0 ⌅ [bca83a33] + OptimizationBase v2.14.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [5ad8b20f] + PhysicalConstants v0.2.4 [2dfb63ee] + PooledArrays v1.4.3 [d236fae5] + PreallocationTools v0.4.34 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 ⌅ [08abe8d2] + PrettyTables v2.4.0 [33c8b6b6] + ProgressLogging v0.1.5 [92933f4c] + ProgressMeter v1.11.0 [94ee1d12] + Quaternions v0.7.6 [44044271] + RDKitMinimalLib v1.2.0 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v3.39.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [f2b01f46] + Roots v2.2.10 [6038ab10] + Rotations v1.7.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.16 [0bca4576] + SciMLBase v2.124.0 [a6db7da4] + SciMLLogging v1.4.0 [c0aeaf25] + SciMLOperators v1.10.0 [431bcebd] + SciMLPublic v1.0.0 [53ae85a6] + SciMLStructures v1.7.0 [7e506255] + ScopedValues v1.5.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [699a6c99] + SimpleTraits 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LibCURL_jll v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.6.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 31.91s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4534.1 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 4997.7 ms ✓ MacroTools 2061.3 ms ✓ InlineStrings 940.2 ms ✓ Reexport 1635.5 ms ✓ ConstructionBase 825.8 ms ✓ DataValueInterfaces 1998.5 ms ✓ Format 938.2 ms ✓ Observables 1080.7 ms ✓ Calculus 879.9 ms ✓ IterTools 821.7 ms ✓ IntervalSets 815.5 ms ✓ Inflate 620.5 ms ✓ CommonSolve 1129.2 ms ✓ TranscodingStreams 739.6 ms ✓ LaTeXStrings 762.8 ms ✓ ChunkCodecCore 606.9 ms ✓ TestItems 856.7 ms ✓ Statistics 735.9 ms ✓ StaticArraysCore 708.6 ms ✓ ChunkSplitters 746.5 ms ✓ AutoHashEquals 668.2 ms ✓ DataAPI 684.1 ms ✓ SciMLPublic 3221.2 ms ✓ ExproniconLite 904.4 ms ✓ RealDot 1184.1 ms ✓ InvertedIndices 1018.4 ms ✓ InverseFunctions 868.4 ms ✓ CompositionsBase 1095.8 ms ✓ AbstractTrees 874.6 ms ✓ EnumX 1025.2 ms ✓ WorkerUtilities 2165.9 ms ✓ FillArrays 994.2 ms ✓ ExprTools 861.4 ms ✓ UnPack 1021.2 ms ✓ Extents 1288.0 ms ✓ OrderedCollections 1519.4 ms ✓ FunctionWrappers 924.1 ms ✓ HashArrayMappedTries 1378.0 ms ✓ ADTypes 1311.6 ms ✓ ProgressLogging 1092.3 ms ✓ DocStringExtensions 786.6 ms ✓ FastClosures 639.2 ms ✓ IteratorInterfaceExtensions 1807.2 ms ✓ Crayons 946.1 ms ✓ DelimitedFiles 1000.6 ms ✓ NaNMath 1142.1 ms ✓ Requires 1176.9 ms ✓ SuiteSparse 32977.8 ms ✓ Unitful 2781.3 ms ✓ SentinelArrays 1583.3 ms ✓ StructTypes 1085.7 ms ✓ LoggingExtras 1810.4 ms ✓ ProgressMeter 1125.0 ms ✓ Compat 1142.8 ms ✓ Preferences 3466.6 ms ✓ SimpleTraits 1015.5 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1439.3 ms ✓ Measurements 801.1 ms ✓ IntervalSets → IntervalSetsRandomExt 745.3 ms ✓ ConstructionBase → ConstructionBaseIntervalSetsExt 895.4 ms ✓ BioGenerics 897.5 ms ✓ CodecZlib 912.2 ms ✓ ChunkCodecLibZlib 1093.4 ms ✓ ChunkCodecLibZstd 1291.7 ms ✓ Statistics → SparseArraysExt 3933.2 ms ✓ FixedPointNumbers 788.5 ms ✓ IntervalSets → IntervalSetsStatisticsExt 978.9 ms ✓ Missings 1017.9 ms ✓ PooledArrays 3303.2 ms ✓ Jieko 1050.1 ms ✓ Quaternions 851.2 ms ✓ InverseFunctions → InverseFunctionsDatesExt 1595.4 ms ✓ InverseFunctions → InverseFunctionsTestExt 790.8 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 858.5 ms ✓ LeftChildRightSiblingTrees 1501.8 ms ✓ FillArrays → FillArraysSparseArraysExt 924.1 ms ✓ FillArrays → FillArraysStatisticsExt 870.6 ms ✓ RuntimeGeneratedFunctions 909.4 ms ✓ Parameters 3360.1 ms ✓ DataStructures 745.5 ms ✓ FunctionWrappersWrappers 859.2 ms ✓ ScopedValues 738.8 ms ✓ ADTypes → ADTypesConstructionBaseExt 1842.0 ms ✓ DifferentiationInterface 759.0 ms ✓ TableTraits 939.6 ms ✓ Adapt 8697.3 ms ✓ FileIO 1736.7 ms ✓ PDMats 1874.5 ms ✓ Unitful → ConstructionBaseUnitfulExt 2089.0 ms ✓ Unitful → PrintfExt 1957.2 ms ✓ Unitful → InverseFunctionsUnitfulExt 912.0 ms ✓ ConsoleProgressMonitor 809.8 ms ✓ Compat → CompatLinearAlgebraExt 870.2 ms ✓ PrecompileTools 1144.2 ms ✓ JLLWrappers 1267.5 ms ✓ SciMLLogging 2979.0 ms ✓ Setfield 1900.1 ms ✓ Measurements → MeasurementsUnitfulExt 2731.1 ms ✓ ColorTypes 17191.2 ms ✓ Moshi 4817.2 ms ✓ Accessors 1970.2 ms ✓ TerminalLoggers 8951.1 ms ✓ SparseConnectivityTracer 1056.6 ms ✓ SortingAlgorithms 1292.0 ms ✓ DifferentiationInterface → DifferentiationInterfaceSparseArraysExt 1761.8 ms ✓ Tables 1122.8 ms ✓ ArrayInterface 1257.4 ms ✓ Adapt → AdaptSparseArraysExt 1154.2 ms ✓ GPUArraysCore 1475.4 ms ✓ FillArrays → FillArraysPDMatsExt 8378.2 ms ✓ UnitfulAtomic 1990.7 ms ✓ FilePathsBase 2473.4 ms ✓ BioSymbols 2906.6 ms ✓ StringManipulation 13244.2 ms ✓ StaticArrays 2738.9 ms ✓ RecipesBase 16169.7 ms ✓ Parsers 11289.7 ms ✓ SparseMatrixColorings 43962.7 ms ✓ JLD2 1445.4 ms ✓ Libffi_jll 1372.0 ms ✓ LZO_jll 1351.0 ms ✓ EarCut_jll 1348.2 ms ✓ Bzip2_jll 1371.3 ms ✓ libinchi_jll 1156.2 ms ✓ Xorg_xtrans_jll 1443.6 ms ✓ boost_jll 1357.4 ms ✓ libpng_jll 1415.7 ms ✓ coordgenlibs_jll 1392.8 ms ✓ L_BFGS_B_jll 1476.1 ms ✓ Libmount_jll 1363.0 ms ✓ Libuuid_jll 1343.2 ms ✓ FriBidi_jll 1306.7 ms ✓ Xorg_libXau_jll 1386.8 ms ✓ Graphite2_jll 1371.7 ms ✓ LLVMOpenMP_jll 1364.8 ms ✓ Libiconv_jll 1306.4 ms ✓ Xorg_libXdmcp_jll 1336.2 ms ✓ Expat_jll 1213.5 ms ✓ ColorTypes → StyledStringsExt 7613.7 ms ✓ Colors 1731.1 ms ✓ Accessors → TestExt 2463.4 ms ✓ Accessors → IntervalSetsExt 2352.4 ms ✓ Accessors → LinearAlgebraExt 1981.4 ms ✓ Accessors → UnitfulExt 2887.7 ms ✓ SparseConnectivityTracer → SparseConnectivityTracerNaNMathExt 1646.1 ms ✓ DifferentiationInterface → DifferentiationInterfaceSparseConnectivityTracerExt 2012.2 ms ✓ TableOperations 764.9 ms ✓ ArrayInterface → ArrayInterfaceStaticArraysCoreExt 1267.2 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 805.9 ms ✓ SciMLStructures 1755.5 ms ✓ PreallocationTools 1045.6 ms ✓ DifferentiationInterface → DifferentiationInterfaceGPUArraysCoreExt 1093.3 ms ✓ ArrayInterface → ArrayInterfaceGPUArraysCoreExt 22215.7 ms ✓ Mendeleev 2619.9 ms ✓ FilePathsBase → FilePathsBaseTestExt 954.7 ms ✓ FilePathsBase → FilePathsBaseMmapExt 25614.1 ms ✓ PrettyTables 4115.0 ms ✓ ArnoldiMethod 1340.0 ms ✓ StaticArrays → StaticArraysStatisticsExt 1404.0 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 5052.0 ms ✓ Rotations 1418.6 ms ✓ DifferentiationInterface → DifferentiationInterfaceStaticArraysExt 1368.3 ms ✓ Adapt → AdaptStaticArraysExt 1500.3 ms ✓ Accessors → StaticArraysExt 1298.1 ms ✓ IntervalSets → IntervalSetsRecipesBaseExt 1292.5 ms ✓ Measurements → MeasurementsRecipesBaseExt 11958.4 ms ✓ BioStructures 13541.8 ms ✓ JSON3 3878.5 ms ✓ JSON 915.3 ms ✓ InlineStrings → ParsersExt 1704.2 ms ✓ DifferentiationInterface → DifferentiationInterfaceSparseMatrixColoringsExt 5248.9 ms ✓ JLD2 → UnPackExt 22859.3 ms ✓ GeometryBasics 1371.6 ms ✓ FreeType2_jll 951.1 ms ✓ LBFGSB 1403.5 ms ✓ Pixman_jll 1075.4 ms ✓ StringEncodings 1433.6 ms ✓ GettextRuntime_jll 1462.6 ms ✓ Xorg_libxcb_jll 1361.3 ms ✓ Graphics 2734.2 ms ✓ SparseMatrixColorings → SparseMatrixColoringsColorsExt 6811.9 ms ✓ Roots 4834.5 ms ✓ SciMLOperators 3634.6 ms ✓ SymbolicIndexingInterface 1994.7 ms ✓ PreallocationTools → PreallocationToolsSparseConnectivityTracerExt 80492.5 ms ✓ DataFrames 9499.5 ms ✓ Graphs 23836.0 ms ✓ CellListMap 1816.0 ms ✓ Rotations → RotationsRecipesBaseExt 2391.6 ms ✓ WeakRefStrings 9617.2 ms ✓ MakieCore 1437.6 ms ✓ RDKit_jll 1492.7 ms ✓ Fontconfig_jll 2603.0 ms ✓ YAML 1356.4 ms ✓ Glib_jll 1200.3 ms ✓ Xorg_libX11_jll 1458.8 ms ✓ Roots → RootsUnitfulExt 775.9 ms ✓ SciMLOperators → SciMLOperatorsStaticArraysCoreExt 1616.0 ms ✓ SciMLOperators → SciMLOperatorsSparseArraysExt 1778.7 ms ✓ SymbolicIndexingInterface → SymbolicIndexingInterfacePrettyTablesExt 3731.3 ms ✓ RecursiveArrayTools 6241.0 ms ✓ BioStructures → BioStructuresDataFramesExt 7984.6 ms ✓ MetaGraphs 26228.6 ms ✓ CSV 941.1 ms ✓ RDKitMinimalLib 1199.8 ms ✓ Xorg_libXrender_jll 1208.2 ms ✓ Xorg_libXext_jll 16025.9 ms ✓ PhysicalConstants 1687.1 ms ✓ RecursiveArrayTools → RecursiveArrayToolsSparseArraysExt 1192.2 ms ✓ RecursiveArrayTools → RecursiveArrayToolsTablesExt 1155.8 ms ✓ RecursiveArrayTools → RecursiveArrayToolsMeasurementsExt 24631.6 ms ✓ SciMLBase 8045.3 ms ✓ BioStructures → BioStructuresGraphsExt 1496.5 ms ✓ Cairo_jll 2600.7 ms ✓ SciMLBase → SciMLBaseMeasurementsExt 2619.3 ms ✓ SciMLBase → SciMLBaseDifferentiationInterfaceExt 1487.2 ms ✓ HarfBuzz_jll 5587.1 ms ✓ OptimizationBase 1447.2 ms ✓ Pango_jll 5369.2 ms ✓ Optimization 2484.4 ms ✓ Cairo 23114.7 ms ✓ MolecularGraph 50235.6 ms ✓ BiochemicalAlgorithms 222 dependencies successfully precompiled in 868 seconds. 37 already precompiled. Precompilation completed after 877.43s ################################################################################ # Testing # Testing BiochemicalAlgorithms Status `/tmp/jl_cuxEA2/Project.toml` [4c88cf16] Aqua v0.8.14 [15f4f7f2] AutoHashEquals v2.2.0 [de9282ab] BioStructures v4.7.0 [3c28c6f8] BioSymbols v5.2.0 [9d651bdf] BiochemicalAlgorithms v0.5.5 [336ed68f] CSV v0.10.15 [69e1c6dd] CellListMap v0.9.14 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [86223c79] Graphs v1.13.1 [0f8b85d8] JSON3 v1.14.3 [c116f080] Mendeleev v1.0.2 [626554b9] MetaGraphs v0.8.1 ⌅ [6c89ec66] MolecularGraph v0.19.1 [510215fc] Observables v0.5.5 ⌅ [7f7a1694] Optimization v4.8.0 [5ad8b20f] PhysicalConstants v0.2.4 ⌅ [08abe8d2] PrettyTables v2.4.0 [94ee1d12] Quaternions v0.7.6 [6038ab10] Rotations v1.7.1 [90137ffa] StaticArrays v1.9.15 [10745b16] Statistics v1.11.1 [856f2bd8] StructTypes v1.11.0 [ab02a1b2] TableOperations v1.2.0 [bd369af6] Tables v1.12.1 [f8b46487] TestItemRunner v1.1.0 [1986cc42] Unitful v1.25.1 [a7773ee8] UnitfulAtomic v1.0.0 [37e2e46d] LinearAlgebra v1.13.0 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_cuxEA2/Manifest.toml` [47edcb42] ADTypes v1.18.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.4.0 [4c88cf16] Aqua v0.8.14 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.22.0 [15f4f7f2] AutoHashEquals v2.2.0 [47718e42] BioGenerics v0.1.5 [de9282ab] BioStructures v4.7.0 [3c28c6f8] BioSymbols v5.2.0 [9d651bdf] BiochemicalAlgorithms v0.5.5 [336ed68f] CSV v0.10.15 [159f3aea] Cairo v1.1.1 [49dc2e85] Calculus v0.5.2 [69e1c6dd] CellListMap v0.9.14 [0b6fb165] ChunkCodecCore v1.0.0 [4c0bbee4] ChunkCodecLibZlib v1.0.0 [55437552] ChunkCodecLibZstd v1.0.0 [ae650224] ChunkSplitters v3.1.2 [944b1d66] CodecZlib v0.7.8 [3da002f7] ColorTypes v0.12.1 [5ae59095] Colors v0.13.1 [38540f10] CommonSolve v0.2.4 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [88cd18e8] ConsoleProgressMonitor v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [a0c0ee7d] DifferentiationInterface v0.7.10 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [411431e0] Extents v0.1.6 [9aa1b823] FastClosures v0.3.2 [5789e2e9] FileIO v1.17.1 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [53c48c17] FixedPointNumbers v0.8.5 [1fa38f19] Format v1.3.7 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v0.1.3 [46192b85] GPUArraysCore v0.2.0 [5c1252a2] GeometryBasics v0.5.10 [a2bd30eb] Graphics v1.1.3 [86223c79] Graphs v1.13.1 [076d061b] HashArrayMappedTries v0.2.0 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.5 [8197267c] IntervalSets v0.7.11 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [033835bb] JLD2 v0.6.2 [692b3bcd] JLLWrappers v1.7.1 ⌅ [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.3 [ae98c720] Jieko v0.2.1 [5be7bae1] LBFGSB v0.4.1 [b964fa9f] LaTeXStrings v1.4.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.1 [e6f89c97] LoggingExtras v1.2.0 [1914dd2f] MacroTools v0.5.16 ⌅ [20f20a25] MakieCore v0.9.5 [eff96d63] Measurements v2.14.1 [c116f080] Mendeleev v1.0.2 [626554b9] MetaGraphs v0.8.1 [e1d29d7a] Missings v1.2.0 ⌅ [6c89ec66] MolecularGraph v0.19.1 [2e0e35c7] Moshi v0.3.7 [77ba4419] NaNMath v1.1.3 [510215fc] Observables v0.5.5 ⌅ [7f7a1694] Optimization v4.8.0 ⌅ [bca83a33] OptimizationBase v2.14.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [5ad8b20f] PhysicalConstants v0.2.4 [2dfb63ee] PooledArrays v1.4.3 [d236fae5] PreallocationTools v0.4.34 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 ⌅ [08abe8d2] PrettyTables v2.4.0 [33c8b6b6] ProgressLogging v0.1.5 [92933f4c] ProgressMeter v1.11.0 [94ee1d12] Quaternions v0.7.6 [44044271] RDKitMinimalLib v1.2.0 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.39.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [f2b01f46] Roots v2.2.10 [6038ab10] Rotations v1.7.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.16 [0bca4576] SciMLBase v2.124.0 [a6db7da4] SciMLLogging v1.4.0 [c0aeaf25] SciMLOperators v1.10.0 [431bcebd] SciMLPublic v1.0.0 [53ae85a6] SciMLStructures v1.7.0 [7e506255] ScopedValues v1.5.0 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 [699a6c99] SimpleTraits v0.9.5 [a2af1166] SortingAlgorithms v1.2.2 [9f842d2f] SparseConnectivityTracer v1.1.2 [0a514795] SparseMatrixColorings v0.4.23 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [69024149] StringEncodings v0.3.7 [892a3eda] StringManipulation v0.4.1 [856f2bd8] StructTypes v1.11.0 ⌃ [2efcf032] SymbolicIndexingInterface v0.3.44 [ab02a1b2] TableOperations v1.2.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [5d786b92] TerminalLoggers v0.1.7 [f8b46487] TestItemRunner v1.1.0 [1c621080] TestItems v1.0.0 [3bb67fe8] TranscodingStreams v0.11.3 [3a884ed6] UnPack v1.0.2 [1986cc42] Unitful v1.25.1 [a7773ee8] UnitfulAtomic v1.0.0 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [ddb6d928] YAML v0.4.15 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.5+0 [5ae413db] EarCut_jll v2.2.4+0 [2e619515] Expat_jll v2.7.3+0 [a3f928ae] Fontconfig_jll v2.17.1+0 [d7e528f0] FreeType2_jll v2.13.4+0 [559328eb] FriBidi_jll v1.0.17+0 [b0724c58] GettextRuntime_jll v0.22.4+0 [7746bdde] Glib_jll v2.86.0+0 [3b182d85] Graphite2_jll v1.3.15+0 [2e76f6c2] HarfBuzz_jll v8.5.1+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [dd4b983a] LZO_jll v2.10.3+0 [81d17ec3] L_BFGS_B_jll v3.0.1+0 [e9f186c6] Libffi_jll v3.4.7+0 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.41.2+0 [38a345b3] Libuuid_jll v2.41.2+0 [36c8627f] Pango_jll v1.56.4+0 ⌅ [30392449] Pixman_jll v0.44.2+0 [03d1d220] RDKit_jll v2022.9.5+0 [4f6342f7] Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] Xorg_libXau_jll v1.0.13+0 [a3789734] Xorg_libXdmcp_jll v1.1.6+0 [1082639a] Xorg_libXext_jll v1.3.7+0 [ea2f1a96] Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 ⌅ [28df3c45] boost_jll v1.76.0+1 [f6050b86] coordgenlibs_jll v3.0.2+0 [172afb32] libinchi_jll v1.6.0+0 [b53b4c65] libpng_jll v1.6.50+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.6.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... ERROR: LoadError: UndefVarError: `push_testset` not defined in `Test` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] getproperty @ ./Base_compiler.jl:50 [inlined] [2] run_tests(path::String; filter::Nothing, verbose::Bool) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:197 [3] kwcall(::@NamedTuple{verbose::Bool}, ::typeof(TestItemRunner.run_tests), path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:133 [4] top-level scope @ ~/.julia/packages/BiochemicalAlgorithms/EdAH5/test/runtests.jl:3 [5] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [6] top-level scope @ none:6 [7] eval(m::Module, e::Any) @ Core ./boot.jl:489 [8] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [9] _start() @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/BiochemicalAlgorithms/EdAH5/test/runtests.jl:3 Testing failed after 83.51s ERROR: LoadError: Package BiochemicalAlgorithms errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1058.32s: package tests unexpectedly errored